@jchodera notes: For example, we have <Residue> denote a residue, <Atom> denotes an atom. The <Protons> tag doesn't denote a proton, but a block of information defining parameters for different titration states.
The suggestion is to rename <TitrationStates/>. Potentially could come up with a term that encompasses tautomers as well, since @wiederm is using the code for that purpose.
Todo:
[ ] Modify the setup code that generates the files
[ ] Modify the code that reads the blocks
[ ] Update any example files (can probably just use sed).
https://github.com/choderalab/protons/blob/master/examples/Ligand%20example/imidazole.xml#L24
@jchodera notes: For example, we have
<Residue>denote a residue,<Atom>denotes an atom. The<Protons> tag doesn't denote a proton, but a block of information defining parameters for different titration states.The suggestion is to rename
<TitrationStates/>. Potentially could come up with a term that encompasses tautomers as well, since @wiederm is using the code for that purpose.Todo:
sed).